对青蒿（Artemisia argyi）的比较基因组分析显示，萜类合成酶的扩展具有不对称性，而青蒿素的生物合成途径则保持相对保守

《The Plant Journal》：Comparative genomic analysis of Artemisia argyi reveals asymmetric expansion of terpene synthases and conservation of artemisinin biosynthesis

本文完成Artemisia argyi染色体水平高分辨率基因组组装，揭示其独特的四倍体进化路径。研究发现该物种经历了染色体融合（Chr8C）和三次全基因组加倍（WGT-1、WGD-3及WGTγ），导致34条染色体和显著基因家族扩张。特别发现ADS同源基因簇（AarADS）在特定染色体上的六聚体串联重复，催化途径与Artemisia annua存在关键差异，解释了其artemisinin合成缺失的分子机制。研究为药用植物基因组进化及分子育种提供新范式。

　　
Artemisia argyi, a renowned medicinal plant in traditional Chinese medicine, has been the subject of extensive genomic research to unravel its evolutionary trajectory and therapeutic potential. This study provides a comprehensive chromosome-level haplotype genome assembly of Artemisia argyi, highlighting its unique evolutionary history and functional divergence in key biosynthetic pathways.

### 1. **Genomic Assembly and Chromosomal Evolution**
The assembled genome spans 7.88 Gb, containing 34 chromosomes (2n=34), which confirms the autotetraploid nature of the species. Evolutionary analysis revealed that the genome originated from a common ancestor with Artemisia annua, undergoing a series of chromosomal rearrangements and whole-genome duplications (WGD). A notable event was the fusion of homologous chromosomes 8A and 8B to form chromosome 8C, followed by a WGD event approximately 1.03 million years ago. This fusion event created an aneuploid intermediate (2n=13+der(7,8,9)), which was stabilized by subsequent genome duplication, leading to the modern tetraploid karyotype.

### 2. **Genomic Features and Comparative Analysis**
The genome exhibits high collinearity with other Artemisia species, particularly Artemisia annua, but significant structural variations were identified. Frequent recombination and multivalent chromosome pairing were observed, suggesting a dynamic genome structure. Comparative analysis with three previously published Artemisia argyi genomes revealed differences in genome size (7.2–8.03 Gb) and structural variations, highlighting the importance of assembling multiple cultivars for accurate genomic reference.

### 3. **Terpene Biosynthesis and TPS Gene Expansion**
The study uncovered a diverse terpene synthase (TPS) gene family, with 451 TPS genes across the genome. These genes underwent multiple rounds of duplication, including recent tandem duplications and segmental expansions, driven by WGD events and independent duplications. A striking finding was the presence of a six-copy tandem cluster of ADS homologs (AarADS) on a single chromosome, which catalyzes the conversion of farnesyl pyrophosphate (FPP) to α-bisabolol. In contrast, Artemisia annua harbors AanADS, which produces amorpha-4,11-diene, a precursor for artemisinin. This functional divergence, supported by heterologous expression in *E. coli* and sequence comparisons, suggests that the ADS gene in Artemisia argyi retained ancestral functions while evolving distinct catalytic outputs.

### 4. **Asymmetrical Evolution and Gene Differentiation**
Following WGD, significant asymmetrical evolution occurred in Artemisia argyi. Allelic gene loss and neofunctionalization were observed across the genome, with 8.34% of genes forming four-allele clusters (ohnologs) and 2.57% showing three-allele clusters. This process was particularly pronounced in the TPS gene family, where 20 loci exhibited four-allele conservation, while 49 loci showed allelic deletions or duplications. Such differentiation influenced metabolic outputs, as seen in the AarADS cluster, which diverged functionally from AanADS despite sharing a conserved enzymatic role.

### 5. **Reproductive and Evolutionary Implications**
The high frequency of multivalent chromosome pairing and recombination in Artemisia argyi suggests mechanisms that promote genetic diversity and chromosome stability. This aligns with the observed rhizome propagation strategy, which may mitigate inbreeding depression in autotetraploids. The genome’s structural plasticity, including inversions and translocations, further underscores the dynamic nature of post-polyploid evolution. These findings have implications for breeding programs, as the genome’s evolutionary history provides insights into adaptive trait acquisition.

### 6. **Functional and Economic Significance**
The identification of AarADS and its functional validation highlights the potential for metabolic engineering in Artemisia species. While AanADS is specialized for artemisinin biosynthesis, AarADS represents a conserved pathway for α-bisabolol production, which has applications in cosmetics and pharmaceuticals. The study also clarified previous misconceptions about the absence of artemisinin in Artemisia argyi, attributing this to functional divergence in ADS homologs rather than a complete loss of biosynthetic pathway genes.

### 7. **Methodological Innovations**
The research employed advanced sequencing and assembly strategies, including PacBio HiFi reads for high-fidelity contig assembly and Hi-C reads for chromosome-level scaffolding. Integration of transcriptomic data (Iso-Seq) and epigenetic analysis improved annotation accuracy. These methodologies set a benchmark for resolving complex genomes in polyploid plants, offering a template for future studies on medicinal crop genomics.

### 8. **Conclusion and Future Directions**
Artemisia argyi’s genome serves as a model for studying autotetraploid evolution, demonstrating how chromosomal fusion and WGD events shape metabolic diversity. The functional divergence of TPS genes and ADS homologs underscores the importance of gene context and evolutionary history in secondary metabolite production. Future research could focus on epigenetic regulation of these genes, as well as cross-species comparisons to identify conserved and species-specific evolutionary strategies.

This study not only advances our understanding of Artemisia argyi’s基因组 evolution but also provides a foundation for optimizing its medicinal value and agricultural utility. The integration of genomic, transcriptomic, and biochemical data offers a multifaceted approach to dissecting plant adaptation mechanisms, with broader applications in crop improvement and pharmaceutical development.